Description

LIM homeobox 9 [Source:HGNC Symbol;Acc:HGNC:14222]

INSDC coordinates

chromosome:GRCh38:CM000663.2:197911902:197935478:1

About this gene

This gene has 8 transcripts (splice variants), 65 orthologues, 11 paralogues, is a member of 4 Ensembl protein families and is associated with 104 phenotypes.

NameTranscript IDbpProteinTranslation IDBiotypeCCDSUniProtRefSeqFlags
LHX9-004ENST000003673877836397aaENSP00000356357
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS1393Q9NQ69 NM_020204
NP_064589
TSL:1

TSL1: All splice junctions of the transcript are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS PI3APPRIS candidate principal isoform (earliest CCDS)
Glossary entry for APPRIS
APPRIS website
LHX9-001ENST000003673907413388aaENSP00000356360
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS30962Q9NQ69 NM_001014434
NP_001014434
TSL:1

TSL1: All splice junctions of the transcript are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS ALT1APPRIS candidate principal isoform that is conserved in at least three tested non-primate species
Glossary entry for APPRIS
APPRIS website
LHX9-007ENST000005611732144336aaENSP00000453064
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0YL54 -TSL:5

TSL5: No single transcript (mRNA or EST) supports this transcript model's structure.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX9-003ENST000003673911623321aaENSP00000356361
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-Q9NQ69 -TSL:5

TSL5: No single transcript (mRNA or EST) supports this transcript model's structure.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX9-005ENST0000036738875854aaENSP00000356358
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0Y330 -TSL:2

TSL2: The best supporting mRNA is flagged as suspect or the support is from multiple ESTs.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX9-009ENST0000060612743137aaENSP00000483170
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-A0A087X083 -CDS 3' incomplete3' truncation in transcript evidence prevents annotation of the end of the CDS.TSL:3

TSL3:The only support for this transcript is from a single EST.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LHX9-006ENST0000047572725926aaENSP00000482898
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-Q9NQ69 -CDS 3' incomplete3' truncation in transcript evidence prevents annotation of the end of the CDS.TSL:1

TSL1: All splice junctions of the transcript are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LHX9-010ENST000006155201051No protein-
 
Retained intronAlternatively spliced transcript that is believed to contain intronic sequence relative to other coding transcripts in a given locus.
---TSL:NA

TSL:NA:The transcript was not analyzed for one of the following reasons:

  • Pseudogene annotation, including transcribed pseudogenes
  • Human leukocyte antigen (HLA) transcript
  • Immunoglobin gene transcript
  • T-cell receptor transcript
  • Single-exon transcript (will be included in a future version)

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

Gene-based displays